De novo assembly |
Cortex |
s |
Insertions, deletions, combinations of SNVs—inversions and deletions—rearrangements |
http://cortexassembler.sourceforge.net/ |
[31] |
SGVar |
s |
Large insertions and deletions, complex SV |
|
[32] |
HySA |
p, s |
Small (11 to 50 bp) to large (> 50 bp) insertions and deletions, complex SV |
https://bitbucket.org/xianfan/hybridassemblysv/overview |
[33] |
Assemblytics |
a |
Insertions and deletions (1 bp to 10 kb), repeat expansions/contractions |
https://github.com/MariaNattestad/Assemblytics |
[34] |
Paftools |
a |
Insertions, deletions |
https://github.com/lh3/minimap2/tree/master/misc |
[35] |
Smartie-sv |
a |
Insertions, deletions, inversions |
https://github.com/zeeev/smartie-sv |
[12] |
BreaKmer |
s |
Insertions, deletions, translocations, inversions, duplications |
https://github.com/ccgd-profile/BreaKmer |
[36] |
novoBreak |
s |
Deletions, duplications, inversions, translocations |
https://sourceforge.net/projects/novobreak/ |
[37] |
Short-read mapping |
BreakDancer |
s |
Deletions, insertions, inversions, intra-chromosomal and inter-chromosomal translocations |
https://github.com/genome/breakdancer |
[38] |
BreakSeq |
|
Insertions, deletions, translocations, inversions, duplications |
http://sv.gersteinlab.org/breakseq/ |
[39] |
CREST |
s |
Insertions, deletions, translocations, inversions, duplications |
https://www.stjuderesearch.org/site/lab/zhang |
[40] |
DELLY |
s |
Deletions, inversions, duplications, inter-chromosomal translocations |
https://github.com/dellytools/delly |
[41] |
EricScript |
s |
Gene fusion |
https://sourceforge.net/projects/ericscript/ |
[42] |
FusionCatcher |
s |
Gene fusion |
https://github.com/ndaniel/fusioncatcher |
[43] |
GRIDSS |
s |
Insertions, deletions, translocations, inversions, duplications |
https://github.com/PapenfussLab/gridss |
[44] |
Gustaf |
s |
Deletions, inversions, duplications, translocation |
http://www.seqan.de/apps/gustaf/ |
[45] |
IDP-fusion |
p, s |
Gene fusion |
https://www.healthcare.uiowa.edu/labs/au/IDP-fusion/ |
[46] |
JAFFA |
p, s |
Gene fusion |
https://github.com/Oshlack/JAFFA/wiki |
[47] |
LUMPY |
s |
Deletions, duplications, inversions, translocations |
https://github.com/arq5x/lumpy-sv |
[48] |
Manta |
s |
Insertions, deletions, translocations, inversions, duplications |
https://github.com/Illumina/manta |
[49] |
Meerkat |
s |
Insertions, deletions, translocations, inversions, duplications |
http://compbio.med.harvard.edu/Meerkat/ |
[50] |
Pindel |
s |
Insertions, deletions, translocations, inversions, duplications |
https://github.com/genome/pindel |
[51] |
STAR-Fusion |
s |
Gene fusion |
https://github.com/STAR-Fusion/STAR-Fusion/wiki |
[52] |
SQUID |
s |
Gene fusion |
https://github.com/Kingsford-Group/squid |
[53] |
TARDIS |
s |
Discovery of tandem and interspersed segmental duplications |
https://github.com/BilkentCompGen/tardis |
[54] |
TIGRA |
s |
Insertions, deletions |
https://bitbucket.org/xianfan/tigra |
[55] |
Tophat-Fusion |
s |
Gene fusion |
http://ccb.jhu.edu/software/tophat/fusion_index.shtml |
[56] |
Ulysses |
s |
Insertions, deletions, translocations, inversions, duplications |
https://github.com/gillet/ulysses |
[57] |
SvABA |
s |
Insertion, deletions, somatic rearrangments |
https://github.com/walaj/svaba |
[58] |
Long-read mapping |
NanoSV |
o |
Local SV (LSV): duplications, deletions, inversions; insertions (transposons, intra-chromosomal (> 1 Mb away) and inter-chromosomal insertions) |
https://github.com/mroosmalen/nanosv |
[59] |
PBHoney |
p |
Insertions, deletions, duplications, inversions, translocations |
https://sourceforge.net/projects/pb-jelly/ |
[60] |
PBSV |
p |
Insertions (20 bp to 5 kb), deletions (20 bp to 100 kb), inversions (200 bp to 5 kb), intra-chromosomal (> 100 kb away) and inter-chromosomal translocations, complex SV |
https://github.com/PacificBiosciences/pbsv |
|
SMRT-SV |
p |
Insertions, deletions, duplications, inversions, translocations |
https://github.com/EichlerLab/pacbio_variant_caller |
[61] |
Sniffles |
o, p |
Insertions, deletions, translocations, inversions, duplications, complex SV (nested SV) |
https://github.com/fritzsedlazeck/Sniffles |
[62] |
Multimethods SV caller |
FusorSV |
s |
Combining LUMPY, DELLY, and GenomeSTRiP |
https://github.com/TheJacksonLaboratory/SVE |
[63] |
MetaSV |
s |
Combining BreakSeq, Breakdancer, Pindel, CNVnator |
http://bioinform.github.io/metasv/ |
[64] |
Parliament2 |
s |
Combining LUMPY, DELLY, Manta, BreakSeq, CNVnator |
https://github.com/dnanexus/parliament2 |
[65] |
SURVIVOR |
a, o, p, s |
Can combine/compare any SVs VCF |
https://github.com/fritzsedlazeck/SURVIVOR |
[10] |
Hi-C technology |
Hic_breakfinder |
h |
Detects SVs based on optical mapping, Hi-C, short reads |
https://github.com/dixonlab/hic_breakfinder |
[66] |
HiCnv |
h |
Pipeline to identify CNVs from Hi-C data |
https://github.com/ay-lab/HiCnv |
[67] |
HiCtrans |
h |
Identify potential translocations using change-point statistics |
https://github.com/ay-lab/HiCtrans |
[67] |
Optical mapping |
|
c |
Commercial tools; visualization and analysis of Bionano data |
https://bionanogenomics.com/support-page/bionano-access-software/ |
|
Strand-Seq technology |
Strandseq-InvertR |
t |
R package to locate putative inversions |
https://sourceforge.net/projects/strandseq-invertr/ |
[68] |
10x Genomics |
Gemtools |
x |
Downstream and in-depth analysis of SVs from linked-read data |
https://github.com/sgreer77/gemtools |
[69] |
GROC-SVs |
x |
Identify large-scale SVs based on barcode information |
https://github.com/grocsvs/grocsvs |
[70] |
LongRanger |
x |
Align reads, call and phase SNPs, indels, identify SVs |
https://support.10xgenomics.com/genome-exome/software/downloads/latest |
[16] |
NAIBR |
x |
Identifies novel adjacencies created by SVs events |
https://github.com/raphael-group/NAIBR |
[71] |